4BXC | pdb_00004bxc

Resolving the activation site of positive regulators in plant phosphoenolpyruvate carboxylase

PDB DOI: https://doi.org/10.2210/pdb4BXC/pdb

Classification: LYASE
Organism(s): Flaveria trinervia
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2013-07-10 Released: 2013-10-02
Deposition Author(s): Schlieper, D., Foerster, K., Paulus, J.K., Groth, G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.86 Å
R-Value Free:
0.221 (Depositor), 0.203 (DCC)
R-Value Work:
0.184 (Depositor)
R-Value Observed:
0.185 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.6 of the entry. See complete history.

Literature

Resolving the Activation Site of Positive Regulators in Plant Phosphoenolpyruvate Carboxylase.

Schlieper, D., Foerster, K., Paulus, J.K., Groth, G.

(2014) Mol Plant 7: 437

PubMed: 24043710 Search on PubMed
DOI: https://doi.org/10.1093/mp/sst130
Primary Citation Related Structures:
4BXC, 4BXH

Organizational Affiliation

Institute of Biochemical Plant Physiology, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University Düsseldorf, 40204 Düsseldorf, Germany.

Macromolecule Content

Total Structure Weight: 227.93 kDa
Atom Count: 14,917
Modeled Residue Count: 1,858
Deposited Residue Count: 1,980
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
C4 PHOSPHOENOLPYRUVATE CARBOXYLASE	A, B	990	Flaveria trinervia	Mutation(s): 0 EC: 4.1.1.31
UniProt
Find proteins for P30694 (Flaveria trinervia) Explore P30694 Go to UniProtKB: P30694
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P30694
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
G6P Query on G6P Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain C [auth A] MOL2 format, chain G [auth B] MOL2 format, chain C [auth A] mmCIF format, chain G [auth B] mmCIF format, chain C [auth A]	C [auth A], G [auth B]	6-O-phosphono-alpha-D-glucopyranose C₆ H₁₃ O₉ P NBSCHQHZLSJFNQ-DVKNGEFBSA-N		Interactions Focus chain C [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B]
TRS Query on TRS Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain D [auth A] MOL2 format, chain H [auth B] MOL2 format, chain D [auth A] mmCIF format, chain H [auth B] mmCIF format, chain D [auth A]	D [auth A], H [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain H [auth B] Interactions & Density Focus chain D [auth A] Focus chain H [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain E [auth A]	E [auth A], I [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain I [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.86 Å
R-Value Free: 0.221 (Depositor), 0.203 (DCC)
R-Value Work: 0.184 (Depositor)
R-Value Observed: 0.185 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 164.413	α = 90
b = 121.232	β = 90
c = 132.186	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2013-10-02

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-10-02
Type: Initial release
Version 1.1: 2013-10-16
Changes: Derived calculations, Other
Version 1.2: 2014-02-05
Changes: Database references
Version 1.3: 2015-07-01
Changes: Data collection
Version 1.4: 2018-03-07
Changes: Data collection, Source and taxonomy
Version 1.5: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Other, Structure summary
Version 1.6: 2023-12-20
Changes: Data collection, Database references, Refinement description, Structure summary